Strain identifier

BacDive ID: 11198

Type strain: Yes

Species: Nocardiopsis halophila

Strain Designation: IQ-H3

Strain history: AS 4.1195 <-- A. M. Al-Tai IQ-H3.

NCBI tax ID(s): 1245472 (strain), 141692 (species)

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General

@ref: 11818

BacDive-ID: 11198

DSM-Number: 44494

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive

description: Nocardiopsis halophila IQ-H3 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from saline soil.

NCBI tax id

NCBI tax idMatching level
141692species
1245472strain

strain history

@refhistory
11818<- JCM <- AS <- A. M. Al-Tai; IQ-H3
67770AS 4.1195 <-- A. M. Al-Tai IQ-H3.

doi: 10.13145/bacdive11198.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis halophila
  • full scientific name: Nocardiopsis halophila Al-Tai and Ruan 1994

  • synonyms

    • @ref: 20215
    • synonym: Nocardiopsis baichengensis

@ref: 11818

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis halophila

full scientific name: Nocardiopsis halophila Al-Tai and Ruan 1994 emend. Nouioui et al. 2018

strain designation: IQ-H3

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colormedium used
69356Brown beige (1011)suter with tyrosine
69356Beige (1001)suter without tyrosine
69356Ivory (1014)ISP 3
69356Light ivory (1015)ISP 4
69356Light ivory (1015), ochre yellow (1024)ISP 7
69356Sand yellow (1002)ISP 2
69356Sand yellow (1002)ISP 5
69356Sand yellow (1002)ISP 6

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
69356yesAerial myceliumPure white (9010)ISP 2
69356yesAerial myceliumSignal white (9003)ISP 3
69356yesAerial myceliumSignal white (9003)ISP 4
69356yesAerial myceliumSignal white (9003)ISP 5
69356noAerial myceliumISP 6
69356noAerial myceliumISP 7
69356yesAerial myceliumSignal white (9003)suter with tyrosine
69356yesAerial myceliumSignal white (9003)suter without tyrosine

pigmentation

@refproductionname
69356noMelanin
69356nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
11818https://www.dsmz.de/microorganisms/photos/DSM_44494.jpgMedium 1240 28°C© Leibniz-Institut DSMZ
69356DSM_44494_image3.pngPlates (1240, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69356DSM_44494_image4.jpegPlates (1240, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11818STARCH-MINERAL SALT-AGAR (STMS) + 10%NACL (DSMZ Medium 1240)yeshttps://mediadive.dsmz.de/medium/1240Name: STARCH-MINERAL SALT-AGAR + 10% NACL (DSMZ Medium 1240) Composition: NaCl 100.0 g/l Agar 15.0 g/l Starch 10.0 g/l (NH4)2SO4 2.0 g/l CaCO3 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 1.0 g/l FeSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l ZnSO4 x 7 H2O 0.001 g/l Distilled water
11818CM + YE MEDIUM (DSMZ Medium 549)yeshttps://mediadive.dsmz.de/medium/549Name: CM + YE MEDIUM (DSMZ Medium 549) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 15.0 g/l Yeast extract 10.0 g/l Casamino acids 7.5 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l FeSO4 x 7 H2O 0.01 g/l HCl 3.646e-05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
11818positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes98.777

halophily

  • @ref: 69356
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H6), MK-10(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6935622599arabinose+growth
6935662968cellulose-growth
6935628757fructose+growth
6935617234glucose+growth
6935617268inositol-growth
6935637684mannose+/-growth
6935616634raffinose-growth
6935626546rhamnose+/-growth
6935617992sucrose+/-growth
6935618222xylose+growth
6837917632nitrate+reduction
683794853esculin-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382alpha-chymotrypsin+3.4.21.1
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69356+-++-+---+/-+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69356+++/-+/-+++/-+/-++/-----+/-+++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11818saline soilIraqIRQAsia
67770Saline soilIraqIRQAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_5741.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_2754;97_3390;98_4275;99_5741&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: AF195411
  • Sequence Identity:
  • Total samples: 59
  • soil counts: 28
  • aquatic counts: 3
  • animal counts: 25
  • plant counts: 3

Safety information

risk assessment

  • @ref: 11818
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Nocardiopsis halophila partial 16S rRNA gene, strain DSM 44494TAJ4210181505ena1245472
20218Nocardiopsis halophila 16S ribosomal RNA gene, partial sequenceAF1954111478ena1245472

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis halophila DSM 444941245472.3wgspatric1245472
66792Nocardiopsis halophila DSM 444942554235470draftimg1245472
67770Nocardiopsis halophila DSM 44494GCA_000341245contigncbi1245472

GC content

  • @ref: 67770
  • GC-content: 73.7
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno92.132no
gram-positiveyes90.158no
anaerobicno99.03no
aerobicyes92.165no
halophileyes63.483no
spore-formingyes93.322no
glucose-utilyes88.078yes
flagellatedno98.46no
thermophileno97.58yes
glucose-fermentno91.247yes

External links

@ref: 11818

culture collection no.: DSM 44494, AS 4.1195, JCM 9892, BCRC 16264, CGMCC 4.1195, KCTC 9825, CCIM A.S.4.1195

straininfo link

  • @ref: 80445
  • straininfo: 50654

literature

  • topic: Phylogeny
  • Pubmed-ID: 31535965
  • title: Genome analysis reveals that Nocardiopsis baichengensis Li et al. 2006 is a later heterotypic synonym of Nocardiopsis halophila Al-Tai and Ruan 1994.
  • authors: Zhang XT, Salam N, Xiao M, Asem MD, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003721
  • year: 2020
  • mesh: Actinobacteria/*classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Genes, Bacterial, Nocardiopsis, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11818Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44494)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44494
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69356Wink, J.https://cdn.dsmz.de/wink/DSM%2044494.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80445Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID50654.1StrainInfo: A central database for resolving microbial strain identifiers